Dear Justin, I have been able to temporarily solve my force field parameter problem (at least test the new parameters). I defined a new Cys residue say CYSA (as anion) in the rtp file. But how can I prevent the pdb2gmx from adding hydrogen to the Cysteine residue? Addition of this extra hydrogen changes all the indexing. Can utilization of an index file during topology generation? or can "grompp -renum" help in this case? I am left wondered how to force pdb2gmx to prompt to ask me for the selection of the type, when several types of a particular residue is defined in the rtp file? Your help is appreciated in advance. Best,
Payman -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Justin Lemkul Sent: January-06-13 6:54 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx On 1/6/13 4:45 PM, Payman Pirzadeh wrote: > Hi, > I am using gromacs 4.5.4, and I am generating a topology file using > G53a5 force field. My protein has a Cys residue which is supposed to > be in thiolate state (negatively charged side chain). During issuing > the pdb2gmx command I use the switch -inter to be prompted about the > charge state of the ionisable side chains, but it asks nothing about > Cys side chains except about they being involved in disulfide bonds. My questions are: > 1. how can I get pdb2gmx ask me about the charge status of Cys > residues? Or do I need to manually change their status in the topology > file and output gro file (removing the HG)? > 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, > the total charge of the residue does not add to -1 but -0.5. Is anyone > aware of any modifications to this force field parameters? I don't know of any. The AMBER force fields have parameters for the thiolate form of cysteine, but I've never seen them for Gromos96 force fields. That doesn't mean they don't exist, of course, but this is the sort of thing one should research prior to choosing a force field and then hoping for a solution later ;) -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
